Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda; Wiser, Andrew H.; Press, Maximilian O.; Langford, Kyle W.; Liachko, Ivan; Snelling, Timothy J.; Dewhurst, Richard J.; Walker, Alan W.; Roehe, Rainer; Watson, Mick

doi:10.1038/s41467-018-03317-6

Cited by 600Genomics and Phylogenetic StudiesRuminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas Production

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

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Stewart, Robert D., Auffret, Marc D., Warr, Amanda, Wiser, Andrew H., Press, Maximilian O., Langford, Kyle W., Liachko, Ivan, Snelling, Timothy J. +4 more·2018·Nature Communications

DOI 10.1038/s41467-018-03317-6PMC PMC5830445

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Abstract

The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. Here we present 913 draft bacterial and archaeal genomes assembled from over 800 Gb of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 69,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 913 genomes presented here improves metagenomic read classification by sevenfold against our own data, and by fivefold against other publicly available rumen datasets. Thus, our dataset substantially improves the coverage of rumen microbial genomes in the public databases and represents a valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.

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Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.
“Subsequently, Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Stewart et al., 2018
Hi-C binning has been used effectively on human feces and in ruminants.
“Hi-C binning has been used effectively on human feces (Press et al., 2017) as well as in ruminants (Stewart et al., 2018).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Stewart et al., 2018

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Watson, M. (2014) · Genome biology · doi:10.1186/gb4165 · Cited by 43 · see citing works
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
Stewart, R. D., Auffret, M. D., Snelling, T. J., Roehe, R., & Watson, M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty905 · Cited by 39 · see citing works
Regulation of fermentation in a ruminal bacterium, Streptococcus bovis, with special reference to rumen acidosis
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Emendation of the Description of Acidaminococcus fermentans, a trans-Aconitate- and Citrate-Oxidizing Bacterium
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Corrigendum: Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibacterium rodentium
Cox, L. M., Sohn, J., Tyrrell, K. L., Citron, D. M., Lawson, P. A., Patel, N. B., Iizumi, T., Perez-Perez, G. I., Goldstein, E. J. C., & Blaser, M. J. (2017) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.002339 · Cited by 32 · see citing works
The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain
Hernandez, J. D., Scott, P. T., SHEPHARD, R., & Jassim, R. A. M. A. (2008) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2007.03696.x · Cited by 24 · see citing works
Bacillus spp. in the rumen ecosystem. Hemicellulose depolymerases and glycoside hydrolases of Bacillus spp. and rumen isolates grown under anaerobic conditions
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Meta4: a web application for sharing and annotating metagenomic gene predictions using web services
Richardson, E. J., Escalettes, F., Fotheringham, I., Wallace, R. J., & Watson, M. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00168 · Cited by 7 · see citing works
Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit
Haley, B. J., Kim, S. W., & Whitehead, T. R. (2016) · Genome Announcements · doi:10.1128/genomea.00978-16 · Cited by 5 · see citing works

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Research works printed but not linked: 1

[24]Stewart, C. S., Flint, H. J. & Bryant, M. P. The Rumen Microbial Ecosystem 10–72 (Springer, Netherlands, 1997).

Sorted by citations

Improved metagenomic analysis with Kraken 2
Wood, D. E., Lu, J., & Langmead, B. (2019) · Genome biology · doi:10.1186/s13059-019-1891-0 · Cited by 7,173 · see citing works
“As databases of assembled genomes continue to grow, databases of reference sequences used for metagenomics studies will also grow [21,23].”
Background
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works
A genomic catalog of Earth’s microbiomes
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N. J., Schulz, F., Wu, D., Páez-Espino, D., Chen, I.-M. A., Huntemann, M., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0718-6 · Cited by 847 · see citing works
“We performed metagenomic assembly and binning on 10,450 globally distributed metagenomes from diverse habitats, including ocean and other aquatic environments (3,345), human and animal host-associated environments (3,536), as well as soils and other terrestrial environments (1,919), to recover 52,515 MAGs (Fig.”
Background
A practical guide to amplicon and metagenomic analysis of microbiome data
Liu, Y., Qin, Y., Chen, T., Lu, M., Qian, X., Guo, X., & Bai, Y. (2020) · Protein & Cell · doi:10.1007/s13238-020-00724-8 · Cited by 875 · see citing works
“…from the human gut (Li et al., 2014; Pasolli et al., 2019; Tierney et al., 2019), the mouse gut (Xiao et al., 2015), the chicken gut (Huang et al., 2018), the cow rumen (Stewart et al., 2018; Stewart et al., 2019), the ocean (Salazar et al., 2019), and the citrus rhizosphere (Xu et al., 2018).”
Background
New insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works
Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments
Karkman, A., Pärnänen, K., & Larsson, D. G. J. (2019) · Nature Communications · doi:10.1038/s41467-018-07992-3 · Cited by 628 · see citing works
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
Stewart, R. D., Auffret, M. D., Warr, A., Walker, A. W., Roehe, R., & Watson, M. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0202-3 · Cited by 593 · see citing works
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
von Meijenfeldt, F. A. B., Arkhipova, K., Cambuy, D. D., Coutinho, F., & Dutilh, B. (2019) · Genome Biology · doi:10.1186/s13059-019-1817-x · Cited by 503 · see citing works
“This database was constructed after the publication of [7].”
Influential
Sequencing-based methods and resources to study antimicrobial resistance
Boolchandani, M., D’Souza, A. W., & Dantas, G. A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0108-4 · Cited by 530 · see citing works
Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle
Li, F., Li, C., Chen, Y., Liu, J., Zhang, C., Irving, B., Fitzsimmons, C., Plastow, G., & Guan, L. L. (2019) · Microbiome · doi:10.1186/s40168-019-0699-1 · Cited by 530 · see citing works
“genomic characters of these heritable rumen taxa, such as the outcomes of the Hungate 1000 project [51] and the 913 microbial genomes assembled from rumen metagenomes [50], will provide more information to explain how host and rumen microorganisms coevolved at the genomic level and provide a better understanding of ho…”
BackgroundMethod
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Sereika, M., Kirkegaard, R. H., Karst, S. M., Michaelsen, T. Y., Sørensen, E. A., Wollenberg, R. D., & Albertsen, M. (2022) · Nature Methods · doi:10.1038/s41592-022-01539-7 · Cited by 478 · see citing works
Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future
Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S. M., Hess, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02161 · Cited by 487 · see citing works
Self-citation
The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency
Matthews, C., Crispie, F., Lewis, E., Reid, M., O’Toole, P. W., & Cotter, P. D. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1505176 · Cited by 466 · see citing works
“This study also highlights the potential to use hybrid short-read and long-read sequencing approaches in order to obtain complete end to end assembly of microbial chromosomes direct from metagenomic data.(100) This approach may involve the use of both Illumina technologies for shorter reads and Pac-Bio or Oxford Nanop…”
Method
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle
Li, F., Hitch, T. C. A., Chen, Y., Creevey, C. J., & Guan, L. L. (2019) · Microbiome · doi:10.1186/s40168-019-0618-5 · Cited by 326 · see citing works
“The sequencing depth of our metagenomes is comparable with the rumen metagenomes published recently, which obtained assembly of 913 near-complete and draft bacterial and archaeal genomes [49].”
BackgroundResult
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314 · see citing works
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
Xie, F., Jin, W., Si, H., Yuan, Y., Tao, Y., Liu, J., Wang, X., Yang, C., Li, Q., Yan, X., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01078-x · Cited by 305 · see citing works
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works
Diverse hydrogen production and consumption pathways influence methane production in ruminants
Greening, C., Geier, R. R., Wang, C., Woods, L. C., Morales, S. E., McDonald, M. J., Rushton-Green, R., Morgan, X. C., Koike, S., Leahy, S. C., et al. (2019) · The ISME Journal · doi:10.1038/s41396-019-0464-2 · Cited by 296 · see citing works
Linking the resistome and plasmidome to the microbiome
Stalder, T., Press, M. O., Sullivan, S. T., Liachko, I., & Top, E. M. (2019) · The ISME Journal · doi:10.1038/s41396-019-0446-4 · Cited by 288 · see citing works
Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns
Weissman, J., Hou, S., & Fuhrman, J. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2016810118 · Cited by 288 · see citing works
Metagenomics-enabled microbial surveillance
Ko, K. K. K., Chng, K. R., & Nagarajan, N. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01089-w · Cited by 275 · see citing works
Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host
Newbold, C. J., & Ramos‐Morales, E. (2020) · animal · doi:10.1017/s1751731119003252 · Cited by 279 · see citing works
New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters
Campanaro, S., Treu, L., Rodriguez‐R, L. M., Kovalovszki, A., Ziels, R. M., Maus, I., Zhu, X., Kougias, P., Basile, A., Luo, G., et al. (2020) · Biotechnology for Biofuels · doi:10.1186/s13068-020-01679-y · Cited by 255 · see citing works
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C
Kent, A. G., Vill, A. C., Shi, Q., Satlin, M. J., & Brito, I. L. (2020) · Nature Communications · doi:10.1038/s41467-020-18164-7 · Cited by 216 · see citing works
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes
Peng, X., Wilken, S. E., Lankiewicz, T. S., Gilmore, S. P., Brown, J. L., Henske, J. K., Swift, C. L., Salamov, A. A., Barry, K., Grigoriev, I. V., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-020-00861-0 · Cited by 227 · see citing works
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
Gilroy, R., Ravi, A., Getino, M., Pursley, I., Horton, D. L., Alikhan, N.-F., Baker, D., Gharbi, K., Hall, N., Watson, M., et al. (2021) · PeerJ · doi:10.7717/peerj.10941 · Cited by 231 · see citing works
The fecal resistome of dairy cattle is associated with diet during nursing
Liu, J., Taft, D. H., Maldonado-Gómez, M. X., Johnson, D., Treiber, M. L., Lemay, D. G., DePeters, E. J., & Mills, D. A. (2019) · Nature Communications · doi:10.1038/s41467-019-12111-x · Cited by 216 · see citing works
New approaches for metagenome assembly with short reads
Ayling, M., Clark, M. D., & Leggett, R. M. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz020 · Cited by 218 · see citing works
“In vivo HiC cross-links DNA within live cells, allowing scaffolding similar to Dove-tail, but uniquely it also allows binning of chromosomes and plasmids in the same original cells [79].”
Background
A metagenomic analysis of the relationship between microorganisms and flavor development in Shaoxing mechanized huangjiu fermentation mashes
Liu, S., Chen, Q., Zou, H., Yu, Y., Zhou, Z., Mao, J., & Zhang, S. (2019) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2019.05.001 · Cited by 213 · see citing works
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M., & McCue, L. A. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03585-4 · Cited by 211 · see citing works
Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis
Hoque, M. N., Istiaq, A., Clement, R. A., Sultana, M., Crandall, K. A., Siddiki, A. Z., & Hossain, M. A. (2019) · Scientific Reports · doi:10.1038/s41598-019-49468-4 · Cited by 197 · see citing works
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
Solden, L., Naas, A. E., Roux, S., Daly, R. A., Collins, W., Nicora, C., Purvine, S. O., Hoyt, D. W., Schückel, J., Jørgensen, B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0225-4 · Cited by 194 · see citing works
Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria
Hitch, T. C. A., Riedel, T., Oren, A., Overmann, J., Lawley, T. D., & Clavel, T. (2021) · ISME Communications · doi:10.1038/s43705-021-00017-z · Cited by 193 · see citing works
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen
Gharechahi, J., Vahidi, M. F., Bahram, M., Han, J., Ding, X., & Salekdeh, G. H. (2020) · The ISME Journal · doi:10.1038/s41396-020-00837-2 · Cited by 189 · see citing works
The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain
Alexa, E. A., Likotrafiti, E., Álvarez-Molina, A., Maradona, M. P., Santos, J. A., & Álvarez‐Ordóñez, A. (2018) · Genes · doi:10.3390/genes9050268 · Cited by 187 · see citing works
A Comprehensive Analysis of the Global Human Gut Archaeome from a Thousand Genome Catalogue
Chibani, C. M., Mahnert, A., Borrel, G., Almeida, A., Werner, A., Brugère, J., Gribaldo, S., Finn, R. D., Schmitz, R. A., & Moissl‐Eichinger, C. (2020) · Nature Microbiology · doi:10.1038/s41564-021-01020-9 · Cited by 183 · see citing works
A roadmap for metagenomic enzyme discovery
Robinson, S. L., Piel, J., & Sunagawa, S. (2021) · Natural Product Reports · doi:10.1039/d1np00006c · Cited by 186 · see citing works
Assembly of hundreds of novel bacterial genomes from the chicken caecum
Glendinning, L., Stewart, R. D., Pallen, M. J., Watson, K., & Watson, M. (2020) · Genome biology · doi:10.1186/s13059-020-1947-1 · Cited by 177 · see citing works
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms
Panel), E. P. O. B. H. (. B., Koutsoumanis, K., Allende, A., Álvarez‐Ordóñez, A., Bolton, D., Bover‐Cid, S., Chemaly, M., Davies, R., Cesare, A. D., Hilbert, F., et al. (2019) · EFSA Journal · doi:10.2903/j.efsa.2019.5898 · Cited by 172 · see citing works
Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses
Gharechahi, J., Vahidi, M. F., Sharifi, G., Ariaeenejad, S., Ding, X., Han, J., & Salekdeh, G. H. (2023) · Environmental Research · doi:10.1016/j.envres.2023.115925 · Cited by 152 · see citing works
Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality
Walsh, A. M., Macori, G., Kilcawley, K. N., & Cotter, P. D. (2020) · Nature Food · doi:10.1038/s43016-020-0129-3 · Cited by 133 · see citing works
Population Genetics in the Human Microbiome
Garud, N. R., & Pollard, K. S. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.10.010 · Cited by 137 · see citing works
“Assembly is improving with chromatin capture scaffolding [166] and longer reads.”
Background
A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation
Gharechahi, J., & Salekdeh, G. H. (2018) · Biotechnology for Biofuels · doi:10.1186/s13068-018-1214-9 · Cited by 141 · see citing works
Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms
Lapidus, A. L., & Korobeynikov, A. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.613791 · Cited by 134 · see citing works
“A recent cow rumen study (Stewart et al., 2018) analyzed more than 800 Gb of rumen metagenomic sequence data from 43 Scottish cattle that allowed to produce 913 draft assemblies of newly sequenced bacterial and archaeal strains and species.”
Background
Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite
Liu, N., Li, H., Chevrette, M. G., Zhang, L., Cao, L., Zhou, H., Zhou, X. J., Zhou, Z., Pope, P. B., Currie, C. R., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0255-1 · Cited by 135 · see citing works
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Somerville, V., Lutz, S., Schmid, M., Frei, D., Moser, A. I., Irmler, S., Frey, J. E., & Ahrens, C. H. (2019) · BMC Microbiology · doi:10.1186/s12866-019-1500-0 · Cited by 132 · see citing works
Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep
Dong, X., Rattray, J. E., Campbell, D. C., Webb, J., Chakraborty, A., Adebayo, O., Matthews, S., Li, C., Fowler, M. G., Morrison, N., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19648-2 · Cited by 132 · see citing works
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Bickhart, D. M., Watson, M., Koren, S., Panke-Buisse, K., Cersosimo, L. M., Press, M. O., Tassell, C. P. V., Kessel, J. A. S. V., Haley, B. J., Kim, S. W., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1760-x · Cited by 131 · see citing works
“(17) and Hungate 1000(18) 177 assemblies.”
BackgroundMethod
Effects of oregano essential oil on in vitro ruminal fermentation, methane production, and ruminal microbial community
Zhou, R., Wu, J., Lang, X., Liu, L., Casper, D. P., Wang, C., Zhang, L., & Wei, S. (2020) · Journal of Dairy Science · doi:10.3168/jds.2019-16611 · Cited by 130 · see citing works
Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients
Ravi, A., Halstead, F. D., Bamford, A. L., Casey, A., Thomson, N. M., van Schaik, W., Snelson, C., Goulden, R., Foster-Nyarko, E., Savva, G. M., et al. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000293 · Cited by 125 · see citing works
“In addition, in its simplest form, the ability of shotgun metagenomics to link mobile elements to the chromosomes from their host cells is poor, although proximity linkage approaches might overcome this limitation [80].”
Background
Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants
Gruninger, R. J., Ribeiro, G. O., Cameron, A., & McAllister, T. A. (2019) · animal · doi:10.1017/s1751731119000752 · Cited by 119 · see citing works
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Alneberg, J., Karlsson, C. M. G., Divne, A., Bergin, C., Homa, F., Lindh, M. V., Hugerth, L. W., Ettema, T. J. G., Bertilsson, S., Andersson, A. F., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0550-0 · Cited by 113 · see citing works
Metagenomic Analyses of Microbial and Carbohydrate-Active Enzymes in the Rumen of Holstein Cows Fed Different Forage-to-Concentrate Ratios
Wang, L., Zhang, G., Xu, H., Xin, H., & Zhang, Y. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00649 · Cited by 111 · see citing works
Bovine host genome acts on rumen microbiome function linked to methane emissions
Martínez-Álvaro, M., Auffret, M. D., Duthie, C.-A., Dewhurst, R. J., Cleveland, M. A., Watson, M., & Roehe, R. (2022) · Communications Biology · doi:10.1038/s42003-022-03293-0 · Cited by 113 · see citing works
Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Chivian, D. C., Jungbluth, S. P., Dehal, P., Wood‐Charlson, E. M., Canon, R. S., Allen, B. H., Clark, M. M., Gu, T., Land, M., Price, G. A., et al. (2022) · Nature Protocols · doi:10.1038/s41596-022-00747-x · Cited by 109 · see citing works
Altitude influences microbial diversity and herbage fermentation in the rumen of yaks
Fan, Q., Wanapat, M., Yan, T., & Hou, F. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02054-5 · Cited by 111 · see citing works
Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?
Pereira, A. M., Dapkevicius, M. D. L. E., & Borba, A. E. S. (2022) · Animal Microbiome · doi:10.1186/s42523-021-00153-w · Cited by 113 · see citing works
“Indeed, the enrichment in those enzymes observed in Bacteroidales, including Prevotellaceae, Fibrobacteres, and some Clostridiales [63], affords them a competitive advantage justifying its higher abundance in the rumen.”
Background
Interrogating the viral dark matter of the rumen ecosystem with a global virome database
Yan, M., Pratama, A. A., Somasundaram, S., Li, Z., Jiang, Y., Sullivan, M. B., & Yu, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-41075-2 · Cited by 106 · see citing works
“We examined whether animals from the same diet or same breed share more vOTUs compared to animals fed different diets or of different breeds using subsets of data from Stewart et al. 78 and Li et al. 79 respectively.”
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Escobar‐Zepeda, A., Godoy-Lozano, E. E., Raggi, L., Segovia, L., Merino, E., Gutiérrez-Ríos, R.-M., Juárez, K., Licea-Navarro, A. F., Pardo‐López, L., & Sánchez‐Flores, A. (2018) · Scientific Reports · doi:10.1038/s41598-018-30515-5 · Cited by 105 · see citing works
RETRACTED: Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products
Bhujbal, S. K., Ghosh, P., Vijay, V. K., Rathour, R., Kumar, M., Singh, L., & Kapley, A. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.152773 · Cited by 106 · see citing works
Retracted
Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences
López-García, A., Pineda-Quiroga, C., Atxaerandio, R., Pérez, A., Hernández, I., García-Rodríguez, A., & González-Recio, Ó. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03010 · Cited by 102 · see citing works
“The rumen microbiota is largely underrepresented in databases and most of them have not been cultured yet (Stewart et al., 2018).”
Background
Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity
Youngblut, N. D., de la Cuesta‐Zuluaga, J., Reischer, G. H., Dauser, S., Schuster, N., Walzer, C., Stalder, G. L., Farnleitner, A. H., & Ley, R. E. (2020) · mSystems · doi:10.1128/msystems.01045-20 · Cited by 100 · see citing works
“3), followed by Eremiobacterota (9), Proteobacteria 284 (7.”
BackgroundInfluential
The microbiome of the buffalo digestive tract
Feng, T., Wang, T., Gao, N., Liu, Z., Cui, K., Duan, Y., Wu, S., Luo, Y., Li, Z., Yang, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28402-9 · Cited by 101 · see citing works
Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine
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Metagenomic insights into the microbe-mediated B and K2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants
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The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity?
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Ten common issues with reference sequence databases and how to mitigate them
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Hi-C metagenome sequencing reveals soil phage–host interactions
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Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats
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Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome
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Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria
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Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolismPreprint
Stewart, R., Auffret, M. D., Warr, A., Snelling, T. J., Dewhurst, R. J., Walker, A. W., Roehe, R., & Watson, M. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/162578 · Cited by 3 · see citing works
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
Stewart, R. D., Auffret, M. D., Warr, A., Walker, A. W., Roehe, R., & Watson, M. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0202-3 · Cited by 593 · see citing works
Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes
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Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan
Sato, Y., Takebe, H., Oishi, K., Yasuda, J., Kumagai, H., Hirooka, H., & Yoshida, T. (2022) · Microbes and Environments · doi:10.1264/jsme2.me22039 · Cited by 16 · see citing works
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen
Glendinning, L., Genç, B., Wallace, R. J., & Watson, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-81668-9 · Cited by 77 · see citing works

Authors: Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., Liachko, I., Snelling, T. J., Dewhurst, R. J., Walker, A. W., Roehe, R., & Watson, M.
Affiliations: Roslin Institute (GB)
Scotland's Rural College (GB)
University of Aberdeen (GB)
Corresponding author: Watson, Mick
ORCID: Auffret, Marc D.
Warr, Amanda
Press, Maximilian O.
Langford, Kyle W.
Liachko, Ivan
Snelling, Timothy J.
Dewhurst, Richard J.
Walker, Alan W.
Roehe, Rainer
Watson, Mick
Venue: Nature Communications
Publisher: Springer Science and Business Media LLC
Published: 2018-02-28
Volume: 9
Issue: 1
Pages: 870-870
ISSN: 2041-1723 (ISSN-L)
DOI: 10.1038/s41467-018-03317-6
PMC: PMC5830445
OpenAlex: W2786358949
Cited by: 559
References: 83
Citations by year: 2026: 39 · 2025: 48 · 2024: 77 · 2023: 69 · 2022: 64 · 2021: 73 · 2020: 89 · 2019: 73 · 2018: 27
FWCI: 24.09
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
Locations: Nature Communications (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, cc-by)
RePEc: Research Papers in Economics (submittedVersion)
Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: Rural and Environment Science and Analytical Services Division
Scottish Government
Scotland’s Rural College
Directorate for Biological Sciences
Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276, BB/M01844X/1, BB/J004235/1, BB/R015023/1, BB/P013732/1, BB/J004235, BB/N016742/1, BB/ J004243/1, BB/N01720X/1, P013759, BBP013759/1, BBS/E/D/20310000)
National Institute of Allergy and Infectious Diseases (R43AI122654, R44AI122654)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
Keywords: rumen microbiome, draft genome sequence, metagenome binning, Hi-C, cattle, rumen bacteria, rumen archaea, carbohydrate metabolism, biomass-degrading enzymes, metagenome-assembled genomes, read classification
MeSH terms: Animals, Bacteria, Bacterial Proteins, Cattle, Phylogeny, Rumen, Genome, Bacterial, Metagenome, Metagenomics

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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

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